Macrocycles provide intricate shape manifolds that leverage the depth of the modern organic chemistry toolbox. Novel chemistry can be introduced via new bond types and unique torsional angles inaccessible by traditional small molecules and biomolecules. In this work, we investigate the conformational space of a class of biscationic macrocycles in protic and aprotic solvents using a combination of ion-mobility spectrometry mass spectrometry, distance geometry modeling, and quantum mechanical calculations. We identify at least three major conformations of the macrocycles. Two of the conformations are rotational isomers in which the amide (carbonyl amide) N-C bond of the acyl hydrazine can adopt either E- or Z-configuration. The E- and Z-rotational isomers were separately observed in previous X-ray crystallography studies on the same set of macrocycles, but both isomers were never proved to exist for the same molecule. We show that low-dielectric solvents and counterions, such as Cl- or PF6-, appear to stabilize the Z-conformation. Lastly, desolvation of the macrocycles in the absence of bound counterions yields a gas-phase "flat" Z-conformation. Our results suggest that the macrocycles are flexible and behave much like short polypeptides. The combination of ion-mobility spectrometry mass spectrometry and distance geometry modeling provides a versatile and robust approach to unravel fundamental information on the flexible chemical space of macrocycles.